ITR: Accelerated Algorithms for Multiple Time Scale Simulations of Ultraslow Systems: Supercooled Liquids and Biomolecules

波士顿大学的托马斯凯斯，约翰斯特劳布和史蒂芬霍默得到了信息技术研究计划下的化学部和材料研究部的支持，以开发和应用过冷液体和生物分子的多时间尺度模拟算法。正在开发三种不同的算法，用于加速不同局部极小值之间的过渡。这三个过程都依赖于识别复杂分子系统中的局部极小值、跃迁势垒和路径的方法，生物学上有趣的过程可能以不同分子构型之间的缓慢跃迁为特征。在一个更快的时间尺度上的动态过程迅速发生在每个配置和两个配置之间的缓慢过渡。同时精确计算慢速和快速过程对计算化学家和材料科学家来说是一个重大挑战。这项工作融合了技术，数学描述景观附近的一个局部最小值与信息技术方法，允许建模这样的慢事件。 这项研究与旨在使年轻研究人员接触多时间尺度问题的教育活动密切相关。

Thomas Keyes, John Straub, and Steven Homer of Boston University are supported by the Chemistry Division and the Division of Materials Research under the Information Technology Research program to develop and apply algorithms for multiple time scale simulations of supercooled liquids and biomolecules. Three different algorithms are being developed for acceleration of transitions between different local minima. All three depend on methods for identifying local minima, transition barriers, and pathways in complicated molecular systems.Biologically interesting processes may be characterized by slow transitions between dissimilar molecular configurations. Dynamical processes on a much faster time scale occur rapidly within each of the configurations and during the slow transition between the two configurations. A simultaneous accurate accounting of both slow and fast processes represents a significant challenge to computational chemists and materials scientists. This work merges techniques for mathematically describing landscapes near a local minimum with information technology methods to allow for modeling of such slow events. The research is strongly coupled to educational activities that are designed to expose young researchers to the multiple time scale problem.